I am experiencing similar results. I made a nand backup of my current configuration (JB 3.6), then wiped the phone and clean installed JB 3.5 which went ok. I then nand restored to 3.6 and there was a strange new option in recovery after the restore process completed. Something like..."your new rom may replace cwm with the stock recovery". Then it gave some option to flash recovery. I wasn't sure what it was so I just used the "go back" option and it automatically rebooted me to system...aaaaand I've been on the boot animation for the last 10 minutes now. Going to pull the battery and retry, if not I'll reflash a JB rom from scratch. Will keep the thread updated but until then
I agree with Steven/Dread. Don't use the 6.x versions of cwm at this time.